Mercurial > repos > yating-l > hubarchivecreatortest
diff hubArchiveCreator.xml @ 1:85195e0d4b71 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
| author | yating-l |
|---|---|
| date | Fri, 29 Sep 2017 13:32:23 -0400 |
| parents | |
| children | fa990284327b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hubArchiveCreator.xml Fri Sep 29 13:32:23 2017 -0400 @@ -0,0 +1,1342 @@ +<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0"> + <description> + This Galaxy tool permits to prepare your files to be ready for + Assembly Hub visualization. + </description> + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + <requirement type="package" version="340">ucsc_hac</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="340">ucsc_bigwig</requirement> + <requirement type="package" version="340">ucsc_bigbed</requirement> + </requirements> + + <stdio> + <regex match="^pass1" + source="stderr" + level="log" + description="bedToBigBed"/> + <!-- TODO: Add the case pass1 and 0 chroms --> + <!-- TODO: Add the case pass2 and 0 records or 0 fields --> + </stdio> + + <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p $output.extra_files_path; + + ## Dump the tool parameters into a JSON file + python $json_file parameters.json; + + python $__tool_directory__/hubArchiveCreator.py --data_json parameters.json -o $output; + + + ]]></command> + <configfiles> + <configfile name="json_file"> +import json +import sys + +file_path = sys.argv[1] +#set global $data_parameter_dict = {} + +## Ask the user to enter the genome name +#silent $data_parameter_dict.update({"genome_name": str($genome_name)}) + +## Function to retrieve the data of the inputs +#def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={}) + #set false_path = str($input_to_prepare) + #set $data_dict = {"false_path": $false_path} + + #set name = str($input_to_prepare.name) + #silent $data_dict.update({"name": $name}) + #silent $data_dict.update($extra_data_dict) + ## Add the ordering by taking the tool form indexes + #silent $data_dict.update({"order_index": $order_index}) + + #if $datatype in $data_parameter_dict + #silent $data_parameter_dict[$datatype].append($data_dict) + #else + #set array_inputs = [] + #silent $array_inputs.append($data_dict) + #silent $data_parameter_dict.update({$datatype: $array_inputs}) + #end if +#end def + +## Get the number of digits from tracks, to have a unique integer from group index and track index + +#set temp_max_digit = 0 + +#for $g in $group + #if len($g.format) > $temp_max_digit + #silent temp_max_digit = len($g.format) + #end if +#end for + + +#set nb_digits_max_track = len(str($temp_max_digit)) + +## END Get the number of digits + +#for $i_g, $g in enumerate( $group ) + #for $i, $f in enumerate( $g.format ) + ## Create the order index using index_group+1 concatenated with index_track + #set index_group_final = str($i_g + 1) + #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) + + ## For each format, we have a few mandatory fields we store in a dict + #set track_color = str($f.formatChoice.track_color) + #set group_name = str($g.group_name) + #set longLabel = str($f.formatChoice.longLabel) + #set extra_data_dict = {"track_color": $track_color, + "group_name": $group_name, + "long_label": $longLabel} + + #if $f.formatChoice.format_select == "bam" + #set bam_index = $f.formatChoice.BAM.metadata.bam_index + + ## Add Bam format specific fields + #silent $extra_data_dict.update({"index": $bam_index}) + + #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bed" + #if $f.formatChoice.bedChoice.bed_select == "bed_generic" + #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand" + #silent $prepare_json("CytoBand", $f.formatChoice.bedChoice.BED_cytoBand, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" + #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" + #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" + #set database = str($f.formatChoice.bedChoice.database) + #silent $extra_data_dict.update({"database": $database}) + #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" + #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id) + #silent $extra_data_dict.update({"trix_id": $trix_id}) + #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection" + #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix) + #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx) + #else + #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix) + #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx) + #end if + #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) + #end if + #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" + #set database = str($f.formatChoice.bedChoice.database) + #silent $extra_data_dict.update({"database": $database}) + #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" + #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id) + #silent $extra_data_dict.update({"trix_id": $trix_id}) + #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection" + #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix) + #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx) + #else + #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix) + #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx) + #end if + #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) + #end if + #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, + $extra_data_dict) + #end if + #end if + #if $f.formatChoice.format_select == "psl" + #silent $prepare_json("Psl", $f.formatChoice.PSL, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bigwig" + #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bigbed" + #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes" + #set trix_id = str($f.formatChoice.add_trix_index.trix_id) + #silent $extra_data_dict.update({"trix_id": $trix_id}) + #if $f.formatChoice.add_trix_index.index_files.index_files_type == "collection" + #set ix_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ix) + #set ixx_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ixx) + #else + #set ix_index = str($f.formatChoice.add_trix_index.index_files.index_ix) + #set ixx_index = str($f.formatChoice.add_trix_index.index_files.index_ixx) + #end if + #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) + #end if + #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "gff3" + #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "gtf" + ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 + #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final, + $extra_data_dict) + #end if + #end for +#end for + +## We combine the fasta file dataset name with his false path in a JSON object +#set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)} +$data_parameter_dict.update({"fasta": $fasta_json}) + +## Retrieve the user email +#silent $data_parameter_dict.update({"user_email": str($__user_email__)}) + +#silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)}) + +#silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)}) + +#silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)}) + +with open(file_path, 'w') as f: + json.dump($data_parameter_dict, f) + + </configfile> + </configfiles> + + <inputs> + <param + name="genome_name" + type="text" + size="30" + value="unknown" + label="UCSC Genome Browser assembly ID" + /> + <param + format="fasta" + name="fasta_file" + type="data" + label="Reference genome" + /> + <repeat name="group" title="New group"> + <param type="text" name="group_name" label="Group name" value="Default group"/> + <repeat name="format" title="New track"> + <conditional name="formatChoice"> + <param name="format_select" type="select" label="Format"> + <option value="bam" selected="true">BAM</option> + <option value="bed">BED</option> + <option value="psl">PSL</option> + <option value="bigwig">BIGWIG</option> + <option value="bigbed">BIGBED</option> + <option value="gff3">GFF3</option> + <option value="gtf">GTF</option> + </param> + + <when value="bam"> + <param + format="bam" + name="BAM" + type="data" + label="BAM File" + /> + <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> + <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="bed"> + <conditional name="bedChoice"> + <param name="bed_select" type="select" label="Bed Choice"> + <option value="bed_generic" selected="true">BED Generic (bed4)</option> + <option value="bed_cytoBand">cytoBand Track (bed4+1)</option> + <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> + <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> + <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option> + <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option> + </param> + <when value="bed_generic"> + <param + format="bed" + name="BED" + type="data" + label="Generic Bed File Choice" + /> + + </when> + <when value="bed_cytoBand"> + <param + format="bed" + name="BED_cytoBand" + type="data" + label="cytoBand Track (Bed4)" + /> + </when> + <when value="bed_simple_repeats_option"> + <param + format="bed" + name="BED_simple_repeats" + type="data" + label="Bed Simple Repeats (Bed4+12) File" + /> + </when> + <when value="bed_splice_junctions_option"> + <param + format="bed" + name="BED_splice_junctions" + type="data" + label="Bed Splice Junctions (Bed12+1) File" + /> + </when> + <when value="bed_blast_alignment_option"> + <param + format="bed" + name="BED_blast_alignment" + type="data" + label="Bed Blast Alignments (Bed12+12) File" + /> + <param name="database" type="select" label="Protein database"> + <option value="NCBI" selected="true">NCBI</option> + <option value="UniProt">UniProt</option> + <option value="FlyBase">FlyBase</option> + <option value="Others">Others</option> + </param> + <expand macro="add_trix_file"/> + </when> + <when value="bed_blat_alignment_option"> + <param + format="bed" + name="BED_blat_alignment" + type="data" + label="Bed BLAT Alignments (bigPsl) File" + /> + <param name="database" type="select" label="mRNA database"> + <option value="NCBI" selected="true">NCBI</option> + <option value="Others">Others</option> + </param> + <expand macro="add_trix_file"/> + </when> + </conditional> + <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="psl"> + <param + format="psl" + name="PSL" + type="data" + label="PSL File" + /> + <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="bigwig"> + <param + format="bigwig" + name="BIGWIG" + type="data" + label="BIGWIG File" + /> + <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="bigbed"> + <param + format="bigbed" + name="BIGBED" + type="data" + label="BIGBED File" + /> + <expand macro="add_trix_file"> + <expand macro="specify_search_index" /> + </expand> + <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="gff3"> + <param + format="gff3" + name="GFF3" + type="data" + label="GFF3 File" + /> + <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="gtf"> + <param + format="gtf" + name="GTF" + type="data" + label="GTF File" + /> + <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </repeat> + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Advanced options"> + <option value="off" selected="true">Hide advanced options</option> + <option value="on">Display advanced options</option> + </param> + <!-- TODO: Avoid redundancy here --> + <when value="on"> + <param name="debug_mode" type="select" label="Activate debug mode"> + <option value="false" selected="true">No</option> + <option value="true">Yes</option> + <help> + Use this option if you are a G-OnRamp developer + </help> + </param> + </when> + <when value="off"> + <param name="debug_mode" type="hidden" + value="false"> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data format="trackhub" name="output"/> + </outputs> + + <tests> + <!-- Test with only the fasta file --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <output name="output" file="only_genome/only_genome.html"> + <!-- Use macro to check the whole common structure without repeated code --> + <expand macro="verify_hub_structure_no_track" test="only_genome" /> + </output> + </test> + + <!-- Test with Bam --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" /> + <param name="longLabel" value="HISAT sequence alignment" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="bam/bam.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + compare="sim_size" + /> + <!-- Use macro to check the whole common structure without repeated code --> + <expand macro="verify_hub_structure" test="bam" /> + </output> + </test> + + <!-- Test with Bed Generic --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_generic"/> + <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/> + <param name="longLabel" value="TBLASTN alignment" /> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_generic/bed_generic.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="bed_generic" /> + </output> + </test> + + <!-- Test with Bed Simple repeat --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_simple_repeats_option"/> + <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/> + <param name="longLabel" value="Simple repeat" /> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="bed_simple_repeats" /> + </output> + </test> + + <!-- Test with Psl --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="psl"/> + <param name="PSL" value="psl/inputs/blastXmlToPsl"/> + <param name="longLabel" value="BLAST Alignment" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="psl/psl_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/blastXmlToPsl.bb" + value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="psl" /> + </output> + </test> + + <!-- Test with BigWig --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> + <param name="longLabel" value="RNA-Seq Coverage" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="bigwig/bigwig.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="bigwig" /> + <!-- check additional trackDb settings for BigWig --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="autoScale"/> + <has_text text="maxHeightPixels"/> + <has_text text="windowingFunction"/> + </assert_contents> + </extra_files> + </output> + </test> + + <!-- Test with GFF3 --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> + <param name="longLabel" value="Augustus" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="gff3/gff3_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="gff3" /> + </output> + </test> + + <!-- Test with GTF --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="longLabel" value="StringTie transcripts" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="gtf/gtf_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="gtf" /> + </output> + </test> + + <!-- Test with BLAT Alignment --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_blat_alignment_option"/> + <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/> + <param name="longLabel" value="BLAT alignment" /> + <param name="track_color" value="#000000"/> + <param name="database" value="NCBI" /> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" + value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="bed_blat_alignment" /> + <!-- check additional trackDb settings for BLAT --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="searchIndex"/> + <has_text text="url"/> + <has_text text="urlLabel"/> + <has_text text="iframeUrl"/> + <has_text text="iframeOptions"/> + </assert_contents> + </extra_files> + </output> + </test> + + <!-- Test with BLAST Alignment --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_blast_alignment_option"/> + <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/> + <param name="longLabel" value="BLAST alignment" /> + <param name="track_color" value="#000000"/> + <param name="database" value="NCBI" /> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" + value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="bed_blast_alignment" /> + <!-- check additional trackDb settings for BLAST --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="searchIndex"/> + <has_text text="url"/> + <has_text text="urlLabel"/> + <has_text text="iframeUrl"/> + <has_text text="iframeOptions"/> + </assert_contents> + </extra_files> + </output> + </test> + + <!-- Test with Regtools Splice Junctions --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_splice_junctions_option"/> + <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/> + <param name="longLabel" value="Splice junctions" /> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/regtools_junctions.bb" + value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="bed_splice_junctions" /> + </output> + </test> + + <!-- Test with Cytoband --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_cytoBand"/> + <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/> + <param name="longLabel" value="Cytoband" /> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_cytoband/cytoband_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/Cytoband.bb" + value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="bed_cytoband" /> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="track cytoBandIdeo"/> + </assert_contents> + </extra_files> + </output> + </test> + + <!-- Test with bigBed --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigbed"/> + <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" /> + <param name="longLabel" value="bigBed" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="big_bed/bigbed_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" + value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="big_bed" /> + </output> + </test> + + <!-- Test with one group and multiple tracks --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="gtf_gff/gtf_gff_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="gtf_gff" /> + </output> + </test> + + <!-- Test with one group and all the supported datatypes --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed"/> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_generic"/> + <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed"/> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_simple_repeats_option"/> + <param name="BED_simple_repeats" ftype="bed" + value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="psl"/> + <param name="PSL" value="psl/inputs/blastXmlToPsl"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_cytoBand"/> + <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_splice_junctions_option"/> + <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_blast_alignment_option"/> + <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/> + <param name="track_color" value="#000000"/> + <param name="database" value="NCBI" /> + </conditional> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_blat_alignment_option"/> + <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/> + <param name="track_color" value="#000000"/> + <param name="database" value="NCBI" /> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="all_datatypes/all_datatypes_trackhub.html"> + <!-- verify tracks folder contains all the files --> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/blastXmlToPsl.bb" + value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Cytoband.bb" + value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/regtools_junctions.bb" + value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" + value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" + value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="all_datatypes" /> + </output> + </test> + + <!-- Test with two groups and no tracks --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + </repeat> + <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html"> + <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" /> + </output> + </test> + + <!-- Test with two groups and one track in first --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + </repeat> + <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html"> + <!-- Check tracks exist --> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="two_groups_one_track_first" /> + </output> + </test> + + <!-- Test with two groups and one track in both --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html"> + <!-- Check tracks exist --> + <!-- First group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + compare="sim_size" + /> + + <!-- Second group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="two_groups_one_track_both" /> + <!-- Check the groups.txt exists and is properly populated --> + </output> + </test> + + <!-- Test with two groups and multiple tracks in both --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html"> + <!-- Check tracks exist --> + <!-- First group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + compare="sim_size" + /> + + <!-- Second group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" + value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" /> + </output> + </test> + + <!-- Test default color in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="default_color/default_color_trackhub.html"> + <expand macro="verify_hub_structure" test="default_color" /> + <!-- Verify trackDb.txt contains the color 0,0,0 --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="color 0,0,0"/> + </assert_contents> + </extra_files> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test changed color in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#8064a2"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="changed_color/changed_color_trackhub.html"> + <expand macro="verify_hub_structure" test="changed_color" /> + <!-- Verify trackDb.txt contains the color 128,100,162 --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="color 128,100,162"/> + </assert_contents> + </extra_files> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test for StringTie Chromosome end coordinates --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" /> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test default label in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="default_color/default_color_trackhub.html"> + <expand macro="verify_hub_structure" test="default_color" /> + <!-- Verify trackDb.txt contains default label --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="longLabel HISAT2 Accepted Hits.bam"/> + </assert_contents> + </extra_files> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test customized label in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="longLabel" value="HISAT sequence alignment" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="changed_label/changed_label_trackhub.html"> + <expand macro="verify_hub_structure" test="changed_label" /> + <!-- Verify trackDb.txt contains the customized label --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="longLabel HISAT sequence alignment"/> + </assert_contents> + </extra_files> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + + + + <!-- Test for big files? --> + + <!-- Find tests that should fail --> + + </tests> + + <help> + This Galaxy tool permits to prepare your files to be ready for + Assembly Hub visualization. + </help> + + <citations> + <citation type="doi">10.7490/f1000research.1112719.1</citation> + </citations> +</tool>